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Protein Structures and Oligomeric States

Enter a protein name, UniProt accession or PDB ID. Name searches ask you to confirm the protein identity before related structures are queried.

Current Protein Identity：P28504 New Search
55PDB entries
56Biological assembly
56chain/assembly records
Main Difference Dimensions in This Set
Different construct Different mutation/modification Different assembly state Different ligand/ion Different experimental conditions Different structure-quality metrics

Difference tags compare only the current result set; every original PDB and assembly record remains separate.

Related-Structure Differences

Each row represents one biological assembly in one PDB entry; multiple monomers of the same protein are listed separately.

PDB Entry Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Experimental Method Experimental Conditions Structure Quality
1A3B COMPLEX OF HUMAN ALPHA-THROMBIN WITH THE BIFUNCTIONAL BORONATE INHIBITOR BOROLOG1 Deposited 1998-01-20 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain I 49–64（16 aa）
Not recorded T29 TRI166 (BIFUNCTIONAL BORONATE INHIBITOR) × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.15；20% PEG 8000, 0.05 M SODIUM PHOSPHATE, PH 7.15
Resolution 1.80 Å R-free 0.230
1A3E COMPLEX OF HUMAN ALPHA-THROMBIN WITH THE BIFUNCTIONAL BORONATE INHIBITOR BOROLOG2 Deposited 1998-01-21 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain I 49–64（16 aa）
Not recorded T16 BOROLOG2 × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.15；20% PEG 8000, 0.05M SODIUM PHOSPHATE, PH 7.15
Resolution 1.85 Å R-free 0.220
1ABI STRUCTURE OF THE HIRULOG 3-THROMBIN COMPLEX AND NATURE OF THE S' SUBSITES OF SUBSTRATES AND INHIBITORS Deposited 1992-08-24 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain I 53–64（12 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.30 Å
1C1U RECRUITING ZINC TO MEDIATE POTENT, SPECIFIC INHIBITION OF SERINE PROTEASES Deposited 1999-07-21 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain I 55–65（11 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 NA SODIUM ION × 1 BAI (5-AMIDINO-2-BENZIMIDAZOLYL)(2-BENZIMIDAZOLYL)METHANE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.2；THROMBIN WAS PURCHASED FROM HAEMATOLOGIC TECHNOLOGIES, INC. AND ACETYL-HIRUDIN FROM BACHEM. THROMBIN WAS PREPARED AS DESCRIBED (SKRZPCZAK-JANKUN ET AL., 1991) .THROMBIN (1.0 MG/ML IN 50 MM HEPES, 50 % GLYCEROL, PH 7.0) WAS INCUBATED WITH 1.0 MM ACETYL-HIRUDIN, 1.0 MM HEMI-BABIM, 1.0 MM ZN+2 FOR 1 HR AT 4 DEG C. GLYCEROL WAS REMOVED AND THE COMPLEX CONCENTRATED WITH A CENTRICON 10 ( AMICON) TO 8.6 MG/ML AS DETERMINED BY THE BIORAD PROTEIN ASSAY KIT USING BOVINE SERUM ALBUMIN. CRYSTALS OF THROMBIN-ACETYL-HIRUDIN-HEMI-BABIM-ZN+2 WERE GROWN IN HANGING DROPS BY VAPOR DIFFUSION AFTER STREAK SEEDING. THE DROPS WERE MADE FROM 5 MICROLITERS OF COMPLEX AND 5 MICROLITERS OF RESERVOIR SOLUTION ( 0.10 M TRIS,0.50 M NACL, 22 % (BY VOLUME) PEG 4K, PH 8.20).
Resolution 1.75 Å R-free 0.235
1C1V RECRUITING ZINC TO MEDIATE POTENT, SPECIFIC INHIBITION OF SERINE PROTEASES Deposited 1999-07-21 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain I 55–65（11 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 2 NA SODIUM ION × 1 BAB BIS(5-AMIDINO-BENZIMIDAZOLYL)METHANE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；THROMBIN WAS PURCHASED FROM HAEMATOLOGIC TECHNOLOGIES, INC. AND ACETYL-HIRUDIN FROM BACHEM. THROMBIN WAS PREPARED AS DESCRIBED (SKRZPCZAK-JANKUN ET AL., 1991) .THROMBIN (1.0 MG/ML IN 50 MM HEPES, 50 % GLYCEROL, PH 7.0) WAS INCUBATED WITH 1.0 MM ACETYL-HIRUDIN, 1.0 MM BABIM, 1.0 MM ZN+2 FOR 1 HR AT 4 DEG C. GLYCEROL WAS REMOVED AND THE COMPLEX CONCENTRATED WITH A CENTRICON 10 (AMICON) TO 8.6 MG/ML AS DETERMINED BY THE BIORAD PROTEIN ASSAY KIT USING BOVINE SERUM ALBUMIN. CRYSTALS OF THROMBIN-ACETYL-HIRUDIN-BABIM-ZN+2 WERE GROWN IN HANGING DROPS BY VAPOR DIFFUSION AFTER STREAK SEEDING. THE DROPS WERE MADE FROM 5 MICROLITERS OF COMPLEX AND 5 MICROLITERS OF RESERVOIR SOLUTION (0.10 M TRIS, 0.50 M NACL, 22 % (BY VOLUME) PEG 4K, PH 7.00). A CO-CRYSTAL WAS SOAKED IN 30 % PEG 4K,0.50 M NACL, 0.10 M TRIS, 46 MM ZN+2, PH 7.00, SATURATED IN BABIM AND CONTAINING 2 % DMSO.
Resolution 1.98 Å R-free 0.248
1C1W RECRUITING ZINC TO MEDIATE POTENT, SPECIFIC INHIBITION OF SERINE PROTEASES Deposited 1999-07-21 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain I 55–65（11 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 3 NA SODIUM ION × 1 BAH BIS(5-AMIDINO-2-BENZIMIDAZOLYL)METHANE KETONE HYDRATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 9；THROMBIN WAS PURCHASED FROM HAEMATOLOGIC TECHNOLOGIES, INC. AND ACETYL-HIRUDIN FROM BACHEM. THROMBIN WAS PREPARED AS DESCRIBED (SKRZPCZAK-JANKUN ET AL., 1991) .THROMBIN (1.0 MG/ML IN 50 MM HEPES, 50 % GLYCEROL, PH 7.0) WAS INCUBATED WITH 1.0 MM ACETYL-HIRUDIN, 1.0 MM BABIM, 1.0 MM ZN+2 FOR 1 HR AT 4 DEG C. GLYCEROL WAS REMOVED AND THE COMPLEX CONCENTRATED WITH A CENTRICON 10 (AMICON) TO 8.6 MG/ML AS DETERMINED BY THE BIORAD PROTEIN ASSAY KIT USING BOVINE SERUM ALBUMIN. CRYSTALS OF THROMBIN-ACETYL-HIRUDIN-BABIM-ZN+2 WERE GROWN IN HANGING DROPS BY VAPOR DIFFUSION AFTER STREAK SEEDING. THE DROPS WERE MADE FROM 5 MICROLITERS OF COMPLEX AND 5 MICROLITERS OF RESERVOIR SOLUTION (0.10 M TRIS, 0.50 M NACL, 22 % (BY VOLUME) PEG 4K, PH 7.00). A CO-CRYSTAL WAS SOAKED IN 30 % PEG 4K,0.50 M NACL, 0.10 M TRIS, 0.4 MM ZN+2, PH 9.00, SATURATED IN KETO- BABIM AND CONTAINING 2 % DMSO.
Resolution 1.90 Å R-free 0.242
1C4U SELECTIVE NON ELECTROPHILIC THROMBIN INHIBITORS WITH CYCLOHEXYL MOIETIES. Deposited 1999-09-25 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain 3 55–63（9 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) NA SODIUM ION × 1 IH1 2-[2-(4-BROMO-BENZENESULFONYL)-ETHYL]-1-3-DIOXO-2,3,5,8-TETRAHYDRO-1H-[1,2,4]TRIAZOLO[1,2-A]PYRIDAZINE-5-CARBOXYLIC ACID(4-CARBAMIMIDOYL-CYCLOHEXYLMETHYL)-AMIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；pH 7.5
Resolution 2.10 Å
1C5L STRUCTURAL BASIS FOR SELECTIVITY OF A SMALL MOLECULE, S1-BINDING, SUB-MICROMOLAR INHIBITOR OF UROKINASE TYPE PLASMINOGEN ACTIVATOR Deposited 1999-12-22 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain I 55–64（10 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) NA SODIUM ION × 1 CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.2；Thrombin was purchased from Haematologic Technologies, Inc. and acetyl-hirudin from Bachem. Thrombin was prepared as described (Skrzpczak-Jankun et al., 1991). Thrombin (1.0 mg/ml in 50 mM HEPES, 50 % glycerol, pH 7.0) was incubated with 1.0 mM acetyl-hirudin for 1 hr at 4 deg C. Glycerol was removed and the complex concentrated with a centricon 10 (Amicon) to about 10 mg/ml as determined by the Biorad protein assay kit using bovine serum albumin. Crystals of thrombin-acetyl-hirudin were grown in hanging drops by vapor diffusion after streak seeding. The drops were made from 5 microliters of complex and 5 microliters of reservoir solution (0.10 M Tris, 0.50 M NaCl, 22 % (by volume) PEG 4K, pH 8.20)., VAPOR DIFFUSION
Resolution 1.47 Å R-free 0.236
1C5N STRUCTURAL BASIS FOR SELECTIVITY OF A SMALL MOLECULE, S1-BINDING, SUB-MICROMOLAR INHIBITOR OF UROKINASE TYPE PLASMINOGEN ACTIVATOR Deposited 1999-12-22 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain I 55–64（10 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) NA SODIUM ION × 1 CA CALCIUM ION × 1 ESI 4-IODOBENZO[B]THIOPHENE-2-CARBOXAMIDINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；Thrombin was purchased from Haematologic Technologies, Inc. and acetyl-hirudin from Bachem. Thrombin was prepared as described (Skrzpczak-Jankun et al., 1991). Thrombin (1.0 mg/ml in 50 mM HEPES, 50 % glycerol, pH 7.0) was incubated with 1.0 mM acetyl-hirudin, 10 mM 4-iodobenzo[b]thiophene-2-carboxamidine for 1 hr at 4 deg C. Glycerol was removed andthe complex concentrated with a centricon 10 (Amicon) to about 10 mg/ml as determined by the Biorad protein assay kit using bovine serum albumin. Crystals of thrombin-acetyl-hirudin-4-iodobenzo[b]thiophene-2-carboxamidine were grown in hanging drops by vapor diffusion after streak seeding. The drops were made from 5 microliters of complex and 5 microliters of reservoir solution (0.10 M Tris,0.50 M NaCl, 22 % (by volume) PEG 4K, pH 7.5)., VAPOR DIFFUSION
Resolution 1.50 Å R-free 0.246
1C5O STRUCTURAL BASIS FOR SELECTIVITY OF A SMALL MOLECULE, S1-BINDING, SUB-MICROMOLAR INHIBITOR OF UROKINASE TYPE PLASMINOGEN ACTIVATOR Deposited 1999-12-22 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain I 55–65（11 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) NA SODIUM ION × 1 BEN BENZAMIDINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；Thrombin was purchased from Haematologic Technologies, Inc. and acetyl-hirudin from Bachem. Thrombin was prepared as described (Skrzpczak-Jankun et al., 1991). Thrombin (1.0 mg/ml in 50 mM HEPES, 50 % glycerol, pH 7.0) was incubated with 1.0 mM acetyl-hirudin, 10 mM benzamidine for 1 hr at 4 deg C. Glycerol was removed and the complex concentrated with a centricon 10 (Amicon) to about 10 mg/ml as determined by the Biorad protein assay kit using bovine serum albumin. Crystals of thrombin-acetyl-hirudin-benzmaidine were grown in hanging drops by vapor diffusion after streak seeding. The drops were made from 5 microliters of complex and 5 microliters of reservoir solution (0.10 M Tris, 0.50 M NaCl, 22 % (by volume) PEG 4K, pH 7.5)., VAPOR DIFFUSION
Resolution 1.90 Å R-free 0.262
1D9I STRUCTURE OF THROMBIN COMPLEXED WITH SELECTIVE NON-ELECTOPHILIC INHIBITORS HAVING CYCLOHEXYL MOIETIES AT P1 Deposited 1999-10-27 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain I 55–64（10 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) NA SODIUM ION × 2 00P (5S)-N-[(trans-4-aminocyclohexyl)methyl]-1,3-dioxo-2-[2-(phenylsulfonyl)ethyl]-2,3,5,8-tetrahydro-1H-[1,2,4]triazolo[1,2-a]pyridazine-5-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；298 K；24% PEG 8000 in 0.1M Sodium Phosphate Buffer, protein concentration: 3.5 mg/ml, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.30 Å
1FPC ACTIVE SITE MIMETIC INHIBITION OF THROMBIN Deposited 1994-10-16 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain I 53–64（12 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) 0ZI amino{[(4S)-4-({[5-(dimethylamino)naphthalen-1-yl]sulfonyl}amino)-5-(4-ethylpiperidin-1-yl)-5-oxopentyl]amino}methaniminium × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.30 Å
1GHV A NOVEL SERINE PROTEASE INHIBITION MOTIF INVOLVING A MULTI-CENTERED SHORT HYDROGEN BONDING NETWORK AT THE ACTIVE SITE Deposited 2001-01-22 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain I 55–65（11 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) NA SODIUM ION × 1 120 2-(2-OXO-1,2-DIHYDRO-PYRIDIN-3-YL)-1H-BENZOIMIDAZOLE-5-CARBOXAMIDINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.8；298 K；PEG 4000, NaCl, pH 7.8, vapor diffusion, temperature 298K
Resolution 1.85 Å R-free 0.235
1GHW A NOVEL SERINE PROTEASE INHIBITION MOTIF INVOLVING A MULTI-CENTERED SHORT HYDROGEN BONDING NETWORK AT THE ACTIVE SITE Deposited 2001-01-22 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain I 55–65（11 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) NA SODIUM ION × 1 BMZ 2-(2-HYDROXY-PHENYL)-1H-BENZOIMIDAZOLE-5-CARBOXAMIDINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.3；298 K；PEG 4000, NaCl, pH 7.3, vapor diffusion, temperature 298K
Resolution 1.75 Å R-free 0.234
1GHX A NOVEL SERINE PROTEASE INHIBITION MOTIF INVOLVING A MULTI-CENTERED SHORT HYDROGEN BONDING NETWORK AT THE ACTIVE SITE Deposited 2001-01-22 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain I 55–65（11 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 CA CALCIUM ION × 1 NA SODIUM ION × 1 BMZ 2-(2-HYDROXY-PHENYL)-1H-BENZOIMIDAZOLE-5-CARBOXAMIDINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.3；298 K；PEG 4000, NaCl (soak at pH 8.2), pH 7.3, vapor diffusion, temperature 298K
Resolution 1.65 Å R-free 0.255
1GHY A NOVEL SERINE PROTEASE INHIBITION MOTIF INVOLVING A MULTI-CENTERED SHORT HYDROGEN BONDING NETWORK AT THE ACTIVE SITE Deposited 2001-01-22 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain I 55–65（11 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 3 NA SODIUM ION × 1 CA CALCIUM ION × 1 121 2-(3-HYDROXY-PYRIDIN-2-YL)-1H-BENZOIMIDAZOLE-5-CARBOXAMIDINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.2；298 K；PEG 4000, NaCl, pH 8.2, vapor diffusion, temperature 298K
Resolution 1.85 Å R-free 0.220
1GHY A NOVEL SERINE PROTEASE INHIBITION MOTIF INVOLVING A MULTI-CENTERED SHORT HYDROGEN BONDING NETWORK AT THE ACTIVE SITE Deposited 2001-01-22 Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count
Chain I 55–65（11 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 6 NA SODIUM ION × 2 CA CALCIUM ION × 2 121 2-(3-HYDROXY-PYRIDIN-2-YL)-1H-BENZOIMIDAZOLE-5-CARBOXAMIDINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.2；298 K；PEG 4000, NaCl, pH 8.2, vapor diffusion, temperature 298K
Resolution 1.85 Å R-free 0.220
1GJ4 SELECTIVITY AT S1, H2O DISPLACEMENT, UPA, TPA, SER190/ALA190 PROTEASE, STRUCTURE-BASED DRUG DESIGN Deposited 2001-04-27 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain I 55–65（11 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) NA SODIUM ION × 1 132 6-CHLORO-2-(2-HYDROXY-BIPHENYL-3-YL)-1H-INDOLE-5-CARBOXAMIDINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.8；298 K；PEG 4000, NaCl (soak at pH 9.0), vapor diffusion at 298K, pH 7.8
Resolution 1.81 Å R-free 0.236
1GJ5 SELECTIVITY AT S1, H2O DISPLACEMENT, UPA, TPA, SER190/ALA190 PROTEASE, STRUCTURE-BASED DRUG DESIGN Deposited 2001-04-27 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain I 55–65（11 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) NA SODIUM ION × 1 130 2-(2-HYDROXY-BIPHENYL)-1H-BENZOIMIDAZOLE-5-CARBOXAMIDINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.3；298 K；PEG 4000, NaCl (soak at pH 8.68), vapor diffusion at 298K, pH 7.3
Resolution 1.73 Å R-free 0.233
1IHS CRYSTAL STRUCTURE OF THE COMPLEX OF HUMAN ALPHA-THROMBIN AND NON-HYDROLYZABLE BIFUNCTIONAL INHIBITORS, HIRUTONIN-2 AND HIRUTONIN-6 Deposited 1993-08-04 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain I 49–65（17 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.00 Å
1IHT CRYSTAL STRUCTURE OF THE COMPLEX OF HUMAN ALPHA-THROMBIN AND NON-HYDROLYZABLE BIFUNCTIONAL INHIBITORS, HIRUTONIN-2 AND HIRUTONIN-6 Deposited 1993-08-04 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain I 55–61（7 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.10 Å
1NM6 thrombin in complex with selective macrocyclic inhibitor at 1.8A Deposited 2003-01-09 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain B 55–65（11 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) L86 (11S)-11-BENZYL-6-CHLORO-1,2,10,11,12,13,14,15,16,17,18,19-DODECAHYDRO-5,9-METHANO-2,5,8,10,13,17-BENZOHEXAAZACYCLOHENI COSINE-3,24-DIONE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；298 K；PEG 8000, sodium phosphate, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.80 Å R-free 0.238
1NT1 thrombin in complex with selective macrocyclic inhibitor Deposited 2003-01-28 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain H 55–65（11 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) T76 (6R,21AS)-17-CHLORO-6-CYCLOHEXYL-2,3,6,7,10,11,19,20-OCTAHYDRO-1H,5H-PYRROLO[1,2-K][1,4,8,11,14]BENZOXATETRAAZA-CYCLOHEPTADECINE-5,8,12,21(9H,13H,21AH)-TETRONE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；298 K；PEG 8000, sodium phosphate, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.00 Å
1NY2 Human alpha thrombin inhibited by RPPGF and hirugen Deposited 2003-02-11 Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
Chain 3 55–64（10 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；PEG 4000, ammonium sulphate, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 25K, temperature 298K
Resolution 2.30 Å
1O2G Elaborate Manifold of Short Hydrogen Bond Arrays Mediating Binding of Active Site-Directed Serine Protease Inhibitors Deposited 2003-03-06 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain I 55–65（11 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) NA SODIUM ION × 1 696 3-{5-[AMINO(IMINIO)METHYL]-1H-INDOL-2-YL}-1,1'-BIPHENYL-2-OLATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；2-propanol, PEG 4000, pH 6.5, vapor diffusion at 298 K, pH 6.50
Resolution 1.58 Å R-free 0.250
1QBV CRYSTAL STRUCTURE OF THROMBIN COMPLEXED WITH AN GUANIDINE-MIMETIC INHIBITOR Deposited 1999-04-27 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain E 55–65（11 aa） Fragment：residues 55-65
Non-standard monomer：Yes (specific site not provided by mmCIF) PPX [PHENYLALANINYL-PROLINYL]-[2-(PYRIDIN-4-YLAMINO)-ETHYL]-AMINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；277.15 K；PEG 8000, phosphate, NaCl, NAN3, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K
Resolution 1.80 Å
1SB1 Novel Non-Covalent Thrombin Inhibitors Incorporating P1 4,5,6,7-Tetrahydrobenzothiazole Arginine Side Chain Mimetics Deposited 2004-02-09 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain I 55–63（9 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) NA SODIUM ION × 2 165 N-(BENZYLSULFONYL)-3-CYCLOHEXYLALANYL-N-(2-AMINO-1,3-BENZOTHIAZOL-6-YL)PROLINAMIDE × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.90 Å R-free 0.224
1SL3 crystal structue of Thrombin in complex with a potent P1 heterocycle-Aryl based inhibitor Deposited 2004-03-05 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain B 55–64（10 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) 170 (2-[6-CHLORO-3-{[2,2-DIFLUORO-2-(1-OXIDOPYRIDIN-2-YL)ETHYL]AMINO}-2-OXOPYRAZIN-1(2H)-YL]-N-[5-CHLORO-2-(1H-TETRAZOL-1-YL)BENZYL]ACETAMIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；298 K；PEG 8000, sodium phosphate, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.81 Å R-free 0.240
1TA2 Crystal structure of thrombin in complex with compound 1 Deposited 2004-05-19 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain B 55–65（11 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) 176 1-(2-AMINO-3,3-DIPHENYL-PROPIONYL)-PYRROLIDINE-3-CARBOXYLIC ACID 2,5-DICHLORO-BENZYLAMIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；298 K；PEG 8000, Sodium phosphate, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.30 Å
1TA6 Crystal structure of thrombin in complex with compound 14b Deposited 2004-05-19 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain B 55–65（11 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) 177 1-[2-AMINO-2-CYCLOHEXYL-ACETYL]-PYRROLIDINE-3-CARBOXYLIC ACID 5-CHLORO-2-(2-ETHYLCARBAMOYL-ETHOXY)-BENZYLAMIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；298 K；PEG 8000, Sodium phosphate, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.90 Å
1TMT CHANGES IN INTERACTIONS IN COMPLEXES OF HIRUDIN DERIVATIVES AND HUMAN ALPHA-THROMBIN DUE TO DIFFERENT CRYSTAL FORMS Deposited 1994-05-26 Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
Chain J 53–65（13 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.20 Å
1TWX Crystal structure of the thrombin mutant D221A/D222K Deposited 2004-07-01 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain C 55–65（11 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；298 K；0.1 M sodium phosphate, 26% PEG 8000, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.40 Å R-free 0.268
1VR1 Specifity for Plasminogen Activator Inhibitor-1 Deposited 1998-12-11 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain I 55–64（10 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.6；pH 7.6
Resolution 1.90 Å R-free 0.256
1XM1 Nonbasic Thrombin Inhibitor Complex Deposited 2004-10-01 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain H 55–64（10 aa） Fragment：residues 55-64
Non-standard monomer：Yes (specific site not provided by mmCIF) GAH N-{[(2S)-1-(N-{[4-({[AMINO(IMINO)METHYL]AMINO}METHYL)CYCLOHEXYL]CARBONYL}-3-CYCLOHEXYL-L-ALANYL)AZETIDIN-2-YL]CARBONYL}-L-TYROSYL-N~6~-[AMINO(IMINO)METHYL]-L-LYSINAMIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；291 K；0.1M potassium phosphate, 20%(w/v) PEG 6000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.30 Å R-free 0.266
1YPE Thrombin Inhibitor Complex Deposited 2005-01-31 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain I 55–64（10 aa） Fragment：residues 1-10
Non-standard monomer：Yes (specific site not provided by mmCIF) NA SODIUM ION × 2 UIP (1R,3AS,4R,8AS,8BR)-4-(2-BENZO[1,3]DIOXOL-5-YLMETHYL-1-ETHYL-3-OXO-DECAHYDRO-PYRROLO[3,4-A]PYRROLIZIN-4-YL)-BENZAMIDINE × 1 GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；phasphate buffer, sodium chloride, PEG 8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.81 Å R-free 0.235
1YPG Thrombin Inhibitor Complex Deposited 2005-01-31 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain I 55–64（10 aa） Fragment：residues 1-10
Non-standard monomer：Yes (specific site not provided by mmCIF) UIR (1R,3AS,4R,8AS,8BR)-4-(2-BENZO[1,3]DIOXOL-5-YL-1-CYCLOPROPYL-3-OXO-DECAHYDRO-PYRROLO[3,4-A]PYRROLIZIN-4-YL)-BENZAMIDINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；phosphate buffer, sodium chloride, PEG 8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.80 Å R-free 0.248
1YPJ Thrombin Inhibitor Complex Deposited 2005-01-31 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain I 55–64（10 aa） Fragment：residues 1-10
Non-standard monomer：Yes (specific site not provided by mmCIF) UIB (1R,3AS,4R,8AS,8BR)-4-{5-(PHENYL[1,3]DIOXOL-5-YLMETHYL)-4-ETHYL-2,3,3-TRIMETHYL-6-OXO-OCTAHYDRO-PYRROLO[3,4-C]PYRROL-1-YL}-BENZAMIDINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；phosphate buffer, sodium chloride, PEG 8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.78 Å R-free 0.239
1YPK Thrombin Inhibitor Complex Deposited 2005-01-31 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain I 55–64（10 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) CCR [N-[N-(4-METHOXY-2,3,6-TRIMETHYLPHENYLSULFONYL)-L-ASPARTYL]-D-(4-AMIDINO-PHENYLALANYL)]-PIPERIDINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；phosphate buffer, sodium chloride, PEG 8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.78 Å R-free 0.239
1YPL X-ray crystal structure of thrombin inhibited by synthetic cyanopeptide analogue RA-1008 Deposited 2005-01-31 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain I 55–64（10 aa） Fragment：residues 1-10
Non-standard monomer：Yes (specific site not provided by mmCIF) NA SODIUM ION × 2 RA8 N-(BENZYLSULFONYL)-L-LEUCYL-N-(4-{[AMINO(IMINO)METHYL]AMINO}BUTYL)-L-PROLINAMIDE × 1 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；phosphate buffer, sodium chloride, PEG 8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.85 Å R-free 0.263
1YPM X-ray crystal structure of thrombin inhibited by synthetic cyanopeptide analogue RA-1014 Deposited 2005-01-31 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain I 55–64（10 aa） Fragment：residues 1-10
Non-standard monomer：Yes (specific site not provided by mmCIF) RA4 N-(4-NITROBENZOYL)-L-LEUCYL-N-(4-{[AMINO(IMINO)METHYL]AMINO}BUTYL)-L-PROLINAMIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；phosphate buffer, sodium chloride, PEG 8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.85 Å R-free 0.260
1ZRB Thrombin in complex with an azafluorenyl inhibitor 23b Deposited 2005-05-19 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain B 55–65（11 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) 062 3-AZA-9-HYDROXY-9-FLUORENYLCARBONYL-L-PROLYL-2-AMINOMETHYL-5-CHLOROBENZYLAMIDE, N-OXIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；298 K；PEG 8000, sodium phosphate, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.90 Å R-free 0.279
2GDE Thrombin in complex with inhibitor Deposited 2006-03-16 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain D 55–64（10 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) NA SODIUM ION × 1 SN3 (R)-3-((2S,3R)-1-((2S,3AR,5S,6S,7AS)-2-(2-(1-CARBAMIMIDOYL-2,5-DIHYDRO-1H-PYRROL-3-YL)ETHYLCARBAMOYL)-5,6-DIHYDROXYOCTA HYDRO-1H-INDOL-1-YL)-3-CHLORO-4-METHYL-1-OXOPENTAN-2-YLAMINO)-2-METHOXY-3-OXOPROPYL HYDROGEN SULFATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；298 K；PEG, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.00 Å R-free 0.248
2HGT STRUCTURE OF THE HIRUGEN AND HIRULOG 1 COMPLEXES OF ALPHA-THROMBIN Deposited 1991-06-03 Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
Chain J 54–64（11 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.20 Å
2PKS Thrombin in complex with inhibitor Deposited 2007-04-18 Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
Chain D 55–64（10 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) NA SODIUM ION × 1 G44 4-({[4-(3-METHYLBENZOYL)PYRIDIN-2-YL]AMINO}METHYL)BENZENECARBOXIMIDAMIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；298 K；27% PEG8000, 0.1M SODIUM PHOSPHATE, PH 7.3, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K
Resolution 2.50 Å R-free 0.259
4UD9 Thrombin in complex with 5-chlorothiophene-2-carboxamide Deposited 2014-12-09 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain I 54–65（12 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) NA SODIUM ION × 2 PO4 PHOSPHATE ION × 1 DMS DIMETHYL SULFOXIDE × 2 GOL GLYCEROL × 3 EDO 1,2-ETHANEDIOL × 2 FQI 5-CHLORO-2-THIOPHENECARBOXAMIDE × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；SEE MATERIALS AND METHODS SECTION OF PUBLICATION, pH 7.5
Resolution 1.12 Å R-free 0.141
5AFY Thrombin in complex with 3-chloro-benzamide Deposited 2015-01-27 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain I 54–65（12 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) NA SODIUM ION × 2 WCE 3-CHLORO-BENZAMIDE × 1 DMS DIMETHYL SULFOXIDE × 2 PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；SEE MATERIALS AND METHODS SECTION OF PUBLICATION, pH 7.5
Resolution 1.12 Å R-free 0.138
5AFZ Thrombin in complex with (2R)-2-(benzylsulfonylamino)-N-(2-((4- carbamimidoylphenyl)methylamino)-2-oxo-propyl)-3-phenyl-propanamide Deposited 2015-01-27 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain I 54–65（12 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) NA SODIUM ION × 2 UET N-(BENZYLSULFONYL)-D-PHENYLALANYL-N-(4-CARBAMIMIDOYLBENZYL)GLYCINAMIDE × 1 PO4 PHOSPHATE ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；SEE MATERIALS AND METHODS SECTION OF PUBLICATION, pH 7.5
Resolution 1.53 Å R-free 0.174
6ZUG Crystal Structure of Thrombin in complex with compound10 Deposited 2020-07-22 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain I 54–64（11 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) QPW 2-[(3-chlorophenyl)methylamino]-7-methoxy-~{N}-[[(3~{S})-oxolan-3-yl]methyl]-~{N}-propyl-1,3-benzoxazole-5-carboxamide × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；283 K；0.02 M phosphate buffer pH 7.5, 27% PEG 8000, 100 mM NaCl
Resolution 1.80 Å R-free 0.212
6ZUH Crystal Structure of Thrombin in complex with compound17 Deposited 2020-07-22 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain I 54–64（11 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) N6H [2-[(3-chlorophenyl)methylamino]-7-methoxy-1,3-benzoxazol-5-yl]-(2,2-dimethylmorpholin-4-yl)methanone × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 DMS DIMETHYL SULFOXIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；283 K；0.02 M phosphate buffer pH 7.5, 27% PEG 8000, 100 mM NaCl
Resolution 1.70 Å R-free 0.218
6ZUN Crystal Structure of Thrombin in complex with compound20a Deposited 2020-07-23 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain I 54–64（11 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) QQ5 [2-[(3-chlorophenyl)methylamino]-7-methoxy-1,3-benzoxazol-5-yl]-[(3~{R},4~{R})-3-methyl-4-oxidanyl-piperidin-1-yl]methanone × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；283 K；0.02 M phosphate buffer pH 7.5, 27% PEG 8000, 100 mM NaCl
Resolution 1.79 Å R-free 0.262
6ZUU Crystal structure of Thrombin in complex with compound30 Deposited 2020-07-23 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain I 54–64（11 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) QQN [2-[(3-chlorophenyl)methylamino]-4-methoxy-1,3-benzoxazol-6-yl]-[(3~{R},4~{R})-3-methyl-4-oxidanyl-piperidin-1-yl]methanone × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；283 K；0.02 M phosphate buffer pH 7.5, 27% PEG 8000, 100 mM NaCl
Resolution 1.94 Å R-free 0.212
6ZUW Crystal Structure of Thrombin in complex with compound40 Deposited 2020-07-23 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain I 54–64（11 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) QQK [2-[[(1~{R})-1-(3-chlorophenyl)ethyl]amino]-7-methoxy-1,3-benzoxazol-5-yl]-[(2~{S},5~{R})-5-ethyl-2-(2-hydroxyethyl)-2-methyl-morpholin-4-yl]methanone × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；283 K；0.02 M phosphate buffer pH 7.5, 27% PEG 8000, 100 mM NaCl
Resolution 2.00 Å R-free 0.213
6ZUX Crystal Structure of Thrombin in complex with compound42a Deposited 2020-07-23 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain I 54–64（11 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) QQE [2-[[(1~{R})-1-(3-chlorophenyl)ethyl]amino]-7-methoxy-1,3-benzoxazol-5-yl]-[(2~{S},5~{S})-5-(2-hydroxyethyl)-2-methyl-morpholin-4-yl]methanone × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；283 K；0.02 M phosphate buffer pH 7.5, 27% PEG 8000, 100 mM NaCl
Resolution 1.94 Å R-free 0.206
6ZV7 Crystal Structure of Thrombin in complex with compound42b Deposited 2020-07-24 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain I 54–64（11 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 QQW [2-[[(1~{R})-1-(3-chlorophenyl)ethyl]amino]-7-methoxy-1,3-benzoxazol-5-yl]-[(2~{R},5~{R})-5-(2-hydroxyethyl)-2-methyl-morpholin-4-yl]methanone × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；283 K；0.02 M phosphate buffer pH 7.5, 27% PEG 8000, 100 mM NaCl
Resolution 1.94 Å R-free 0.190
6ZV8 Crystal Structure of Thrombin in complex with compound51 Deposited 2020-07-24 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain I 54–64（11 aa） Fragment：HIRUDIN FRAGMENT
Non-standard monomer：Yes (specific site not provided by mmCIF) QQT [2-[[(1~{S})-1-(3-chlorophenyl)-2-fluoranyl-ethyl]amino]-7-methoxy-1,3-benzoxazol-5-yl]-[(2~{S},5~{S})-5-(2-hydroxyethyl)-2-methyl-morpholin-4-yl]methanone × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；283 K；0.02 M phosphate buffer pH 7.5, 27% PEG 8000, 100 mM NaCl
Resolution 1.70 Å R-free 0.247
9R8Q Structure of thrombin bound to BAY 3389934 Deposited 2025-05-16 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain I 54–64（11 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) A1JDJ 2-(1-methylimidazol-2-yl)ethyl (2~{S})-3-[(5-chloranylthiophen-2-yl)carbonylamino]-2-[[2-ethyl-3-[(3~{S})-3-oxidanyl-2-oxidanylidene-pyrrolidin-1-yl]phenyl]sulfonylamino]propanoate × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 GOL GLYCEROL × 3 DMS DIMETHYL SULFOXIDE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.02M phosphate buffer at pH 7.5, 27% PEG 8000 and 100mM sodium chloride. Thrombin seeds were added to the final drop
Resolution 1.80 Å R-free 0.200

This page presents structural evidence recorded in PDB/mmCIF.“No recorded non-water small molecule” does not prove that the experimental sample was ligand-free; experimental conditions belong to the PDB experiment, while ligands and copy counts are shown for each biological assembly.